PECaller statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PECaller

Tool usage distribution map

This map represents all the scientific publications referring to PECaller per scientific context
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Associated diseases

This word cloud represents PECaller usage per disease context

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PECaller specifications


Unique identifier OMICS_19097
Name PECaller
Alternative name PEMapper
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes




No version available


  • person_outline Stephen Warren
  • person_outline Michael Zwick
  • person_outline David Cutler

Publication for PECaller

PECaller citations


NOX1 loss of function genetic variants in patients with inflammatory bowel disease

PMCID: 5924597
PMID: 29091079
DOI: 10.1038/mi.2017.74
call_split See protocol

[…] E) sequencing. Image processing and base calling was performed using standard Illumina software. Raw sequence reads were mapped relative to the human genome reference sequence (GRCh38/hg38) using the PEMapper software tool (Cutler DJ et al, submitted) to identify single nucleotide variants (SNVs). […]


Genome Wide Association Study to Find Modifiers for Tetralogy of Fallot in the 22q11.2 Deletion Syndrome Identifies Variants in the GPR98 Locus on 5q14.3

Circ Cardiovasc Genet
PMCID: 5647121
PMID: 29025761
DOI: 10.1161/CIRCGENETICS.116.001690
call_split See protocol

[…] Hudson Alpha Institute for Biotechnology (Huntsville, Alabama) as part of the International 22q11.2 Brain and Behavior Consortium to find genes for schizophrenia. Variant calling was performed using PEMapper software for read mapping to the hg38 (GRCh38) reference genome and PECaller software for variant calling. CrossMap ( was used to convert genome coordinates b […]


Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells

Nat Commun
PMCID: 5414116
PMID: 28440315
DOI: 10.1038/ncomms15102
call_split See protocol

[…] me array according to the manufacturer's protocol, and 100-bp paired-end sequencing was performed using an Illumina HiSeq 2000. Raw sequencing reads were mapped to the whole mouse genome (mm10) using PEMapper/PECaller ( with the default settings, and variant bases were annotated with SeqAnt ( For samples subjected to mutat […]


Identification of rare X linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder

Mol Autism
PMCID: 3492087
PMID: 23020841
DOI: 10.1186/2040-2392-3-8
call_split See protocol

[…] Raw base-calling data generated by IGA were used as input for mapping and alignment. Paired-end reads were mapped and variants were called relative to a reference sequence using PEMapper (Cutler DJ et al., in revision). Briefly, the PEMapper is composed of four interconnected programs. The first program prepared a hashed index of the target sequence, the second program genera […]


Genistein cooperates with the histone deacetylase inhibitor vorinostat to induce cell death in prostate cancer cells

BMC Cancer
PMCID: 3472186
PMID: 22494660
DOI: 10.1186/1471-2407-12-145

[…] n kit (Qiagen), and submitted to the Emory Winship Cancer Institute Cancer Genomics Shared Resource for Ion Torrent sequencing, which was performed as described []. Sequencing data was analyzed using PEMapper software (Cutler D, Patel V, Mondal K, Ramachandran D, Steinberg K, Shetty A, Zwick M: PEMapper: A New Approach to Identifying Genetic Variation in Second-Generation Sequencing Studies, submi […]

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PECaller institution(s)
Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA; Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, USA; Division of Neurology, Atlanta Veterans Affairs Medical Center, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA; Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
PECaller funding source(s)
Supported by NIH/National Institute of Mental Health Grants U54 HD082015 and U01 MH101720, which are part of the International Consortium on Brain and Behavior in 22q11.2 Deletion Syndrome, and the Simons Foundation Autism Research Initiative.

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